Trimming customed adaptor sequences with trimmomatic

1

Hello everyone!

Is it possible to trim the customed adaptors using trimmomatic for exon capture sequencing?
If so, how can I create the adaptor fasta file (sequence header etc.)?

The adapters used are below, "BCBCBCBC" stands for the barcodes.

i7: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-BCBCBCBC-ATCTCGTATGCCGTCTTCTGCTTG

i5: AATGATACGGCGACCACCGAGATCTACAC-BCBCBCBC-ACACTCTTTCCCTACACGACGCTCTTCCGATCT

Thank you in advance!


trim


exon


Bioinformatics


trimmomatic


illumina

• 299 views

Are you sure these are truly custom adapters? Generally one looks for the core sequence at the beginning of adapter and then once that is found removes everything to the right of that sequence, which will include BCBCBCBC.

You can use bbduk.sh from BBMap suite with whatever adapters you want to use in a multi-fasta file like bbduk.sh in=your.fq out=clean.fq ref=adapter.fa ..... A guide is available.


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